Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage

Takayuki Tsukamoto, Yuji Mochizuki, Naoki Watanabe, Kaori Fukuzawa, Tatsuya Nakano

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

The reliability of protein structure is a critical concern to grasp the insights with respect to residue-residue and residue-ligand interactions by computational methods. In such calculations, the molecular geometries are usually prepared by the optimization of experimental structure with empirical molecular mechanics (MM) parameters. As an alternative to MM methods, we have developed a partial geometry optimization with the fragment molecular orbital (FMO) scheme at the second-order Møller-Plesset perturbation (MP2) level. The TrpCage miniprotein was used as a demonstrative example. The geometries of the central region were partially optimized at the FMO-MP2 and Hartree-Fock (FMO-HF) levels, and the former with the correlation correction showed reasonable agreement with the experimental structure.

Original languageEnglish
Pages (from-to)157-162
Number of pages6
JournalChemical Physics Letters
Volume535
DOIs
Publication statusPublished - 2012 May 11
Externally publishedYes

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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